I understand that on speed races such as 100m, 200m, up to 10000m men have a physical advantage because of their bigger muscles. But over longer distances that shouldn't matter and women, seems to me, should be able to beat men.

1 Answer
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Mens muscles are stronger. That's the biggest factor. They have stronger muscles, denser bones, mostly related to the effects of testosterone. Women are slower than men by an average of around 10% across all distances.

You can see examples of this split, look at junior and young categories for many sports, and women are just as competitive as men (or boys/girls if you prefer), then once puberty hits, you see the differences start cropping up.

In addition, in general, women have less cardiac output, less hemoglobin per blood volume and also less blood volume then men of comparable size.

All of these add up, and the end result is women are slower than men. You can even look at Caster Semenya, who has both male and female sex organs, and has testosterone ~ 3x the normal level for a woman. Her best times for her events (800m and 1500m) don't even meet the Olympic A standards for males.